We've had our Limited for about half a year now, here's my top list of gripes with what is otherwise an excellent vehicle:
-stock headlights suck - XD 4300K HID kit fixed that, but they were truly disappointing, almost unsafe bad
-rear wiper sucks, why mount it in the spoiler so it has to swing down, leaving the narrowest part of the cleaned area at the top where you're looking through the window?!? All my previous Toyota SUV's have had the wiper at the bottom of the window.
-rear spoiler sucks, impossible to dry up in there after a carwash, always get drips
-Limited trim could have done without the extra chrome, different front and rear bumpers, deeper rocker panels, and 20's, these are all things I'd like to change to match the other trim levels, maybe offer an "UnLimited" with the full time AWD, memory seating, heated/cooled seats, auto headlights, etc that people actually like about the Limited, without all the junk they wish they didn't have to accept to get it?
-too much rake from factory, bring the front up an inch and increase the springrate in the rear if necessary
-no heated steering wheel in the Limited, this one really bugs me for some reason
-no car play in factory head unit, why though?
-throttle by wire calibration, it's just terrible. Sprint Booster makes a big difference, but it's $300 you shouldn't need to spend to fix this issue